tags to format it correctly). Also if you're not already using it I suggest updating to Arduino 1.5.6, the earlier versions had some problems with multiple SPI devices on Due (I saw it with Ethernet & SD concurrently, but it could have also been a problem with other combinations).
Does the SD card work properly if you take the thermocouple out of the equation?
Regards,
Angus

/*
SD card datalogger
This example shows how to log data from three analog sensors
to an SD card using the SD library.
The circuit:
* analog sensors on analog ins 0, 1, and 2
* SD card attached to SPI bus as follows:
** MOSI - pin 11
** MISO - pin 12
** CLK - pin 13
** CS - pin 4
created 24 Nov 2010
modified 9 Apr 2012
by Tom Igoe
This example code is in the public domain.
*/
#include <SD.h>
#include <SPI.h>
// On the Ethernet Shield, CS is pin 4. Note that even if it's not
// used as the CS pin, the hardware CS pin (10 on most Arduino boards,
// 53 on the Mega) must be left as an output or the SD library
// functions will not work.
const int chipSelect = 4;
void setup()
{
// Open serial communications and wait for port to open:
Serial.begin(9600);
while (!Serial) {
; // wait for serial port to connect. Needed for Leonardo only
}
Serial.print("Initializing SD card...");
// make sure that the default chip select pin is set to
// output, even if you don't use it:
pinMode(4, OUTPUT);
// see if the card is present and can be initialized:
if (!SD.begin(chipSelect)) {
Serial.println("Card failed, or not present");
// don't do anything more:
return;
}
Serial.println("card initialized.");
}
void loop()
{
// make a string for assembling the data to log:
String dataString = "";
// read three sensors and append to the string:
for (int analogPin = 0; analogPin < 3; analogPin++) {
int sensor = analogRead(analogPin);
dataString += String(sensor);
if (analogPin < 2) {
dataString += ",";
}
}
// open the file. note that only one file can be open at a time,
// so you have to close this one before opening another.
File dataFile = SD.open("datalog.txt", FILE_WRITE);
// if the file is available, write to it:
if (dataFile) {
dataFile.println(dataString);
dataFile.close();
// print to the serial port too:
Serial.println(dataString);
}
// if the file isn't open, pop up an error:
else {
Serial.println("error opening datalog.txt");
}
}

pinMode(_csTC, OUTPUT); // Setup the _csTC pin for the MAX31855 as an output
digitalWrite(_csTC, HIGH);

Because otherwise as an output it's defaulting to low (asserted), and then when you call SD.begin() the MAX31855 is also enabled for the duration of that SD initialisation sequence, which probably causes it to get into a bad state.

However I have solved the problem in a really UGLY way. I have created a 'throw-away' variable and do an additional SPI transfer before I assert my TC chip select line low. Seems to clear the corrupt data and I get my 2 bytes of temperature data.

I think the problem is probably somewhere in the backend of the SD code. I've noticed there is no SD.end function along the lines of the SPI.end but I don't have time at the moment to delve into the code to find it. My fix will work for getting the data I need to finish my Master's.